Data integration in biological research: an overview

Table 3 Mostly commonly used data formats in bioinformatics

Data format class	General data-	Nucleotide sequence	Protein sequence	Structural	Sequence	Other data
	interchange formats	data	data	data	alignment	types (PPI, etc)
Tabl	CSV, TSV	BED; GFF	GFF, Uniprot-GFF	PSF(D), MMCIF(D)	SAM(D)
FASTA-like		FASTA; FASTQ	FASTA, PIR		SAM(M)	Wig
GenBank-like		GenBank; EMBL	Uniprot-TEXT	PDB, PSF(M), MMCIF(D)	CLUSTAL, MSF,
					PHYLIP(D)
Tag-structured	HTML; XML; JSON	SBOL-XML	Uniprot-XML;			PSI MI-XML;
			Uniprot-RDF/XML			PSI-PAR

D = data; M = metadata. Formats appearing in more than one class are a mixture of classes

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